rs6679677
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (A;A) | 3 | 5.2x risk for T1D; 3.3x for RA |
| (A;C) | 2.3 | 1.8x risk for T1D; 2x risk for RA |
| (C;C) | 0 | normal |
| Reference | GRCh38 38.1/141 |
| Chromosome | 1 |
| Position | 113761186 |
| Gene | PHTF1 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs6679677 |
| dbSNP (classic) | rs6679677 |
| ClinGen | rs6679677 |
| ebi | rs6679677 |
| HLI | rs6679677 |
| Exac | rs6679677 |
| Gnomad | rs6679677 |
| Varsome | rs6679677 |
| LitVar | rs6679677 |
| Map | rs6679677 |
| PheGenI | rs6679677 |
| Biobank | rs6679677 |
| 1000 genomes | rs6679677 |
| hgdp | rs6679677 |
| ensembl | rs6679677 |
| geneview | rs6679677 |
| scholar | rs6679677 |
| rs6679677 | |
| pharmgkb | rs6679677 |
| gwascentral | rs6679677 |
| openSNP | rs6679677 |
| 23andMe | rs6679677 |
| SNPshot | rs6679677 |
| SNPdbe | rs6679677 |
| MSV3d | rs6679677 |
| GWAS Ctlg | rs6679677 |
| GMAF | 0.04132 |
| Max Magnitude | 3 |
| ? | (A;A) (A;C) (C;C) | 28 |
|---|---|---|
|
| ||
rs6679677 has been reported in a large study to be associated with rheumatoid arthritis.
The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.98 (CI 1.72-2.27), and for homozygotes, 3.32 (CI 1.93-5.69). [PMID 17554300
]
rs6679677 was also reported in the same study to be associated with type-1 diabetes.
The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.82 (CI 1.59-2.09), and for homozygotes, 5.19 (CI 3.15-8.55). [PMID 17554300]
Recently (Feb 2008), it has been asserted that the association between rs6679677 and type-1 diabetes is actually completely due to a closely linked, potentially causal variant identified as rs2476601, which is also known as Arg620Trp. In this study, apparently the largest to date, the odds ratio for the risk allele (of rs6679677) was reported to be 1.88 (CI: 1.66-2.13).[PMID 18305142]
DeCode reports that the CC genotype is associated with 1.05x higher odds of Crohn's disease. [PMID 18587394]
| GWAS snp | |
|---|---|
| PMID | [PMID 18978792]
|
| Trait | Type 1 diabetes |
| Title | Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci |
| Risk Allele | A |
| P-val | 1E-40 |
| Odds Ratio | NR NR |
| GWAS snp | |
|---|---|
| PMID | [PMID 18794853]
|
| Trait | Rheumatoid arthritis |
| Title | Common variants at CD40 and other loci confer risk of rheumatoid arthritis |
| Risk Allele | |
| P-val | 6.0000000000000005E-42 |
| Odds Ratio | 1.79 [1.65-1.94] |
| GWAS snp | |
|---|---|
| PMID | [PMID 17554260]
|
| Trait | Type 1 diabetes |
| Title | Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes |
| Risk Allele | A |
| P-val | 7.9999999999999994E-24 |
| Odds Ratio | 1.89 [1.67-2.13] |
[PMID 19565500] Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis
[PMID 22493691] Novel associations for hypothyroidism include known autoimmune risk Loci.
[PMID 18224312] Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.
[PMID 18274536] Genome-wide association studies: progress and potential for drug discovery and development.
[PMID 18533027] Worldwide population differentiation at disease-associated SNPs.
[PMID 18853133] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.
[PMID 19168599] Type 1 diabetes in the BB rat: a polygenic disease.
[PMID 19474294] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
[PMID 19639606] Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases.
[PMID 19956648] Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases.
[PMID 20017963] Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis.
[PMID 20089178] Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population.
[PMID 20722033] The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.
[PMID 20808825] Novel association strategy with copy number variation for identifying new risk Loci of human diseases.
| GWAS snp | |
|---|---|
| PMID | [PMID 23128233]
|
| Trait | Crohn's disease |
| Title | Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. |
| Risk Allele | C |
| P-val | 2E-15 |
| Odds Ratio | 1.20 [1.129-1.268] |
[PMID 28603863] Identification of PTPN22, ST6GAL1 and JAZF1 as Psoriasis Risk Genes Demonstrates Shared Pathogenesis between Psoriasis and Diabetes.
